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SNT: Manual

180 bytes added, 10 June
Tracing on Secondary Image
===Tracing on Secondary Image===
This is one of SNT's most advanced features. [[#Auto-tracing|Hessian-based analysis]] provides a convenient and easy way to perform auto-tracing on pre-process processed data in which voxels defining the traced structure are scored by their likelihood of ''belonging'' to a tube-like structure. However, it is just one approach for "tubeness" classification. What if your data requires different filtering?, or you want to experiment with other approaches?, or the perfect pre-processing algorithm for your images is not yet available in ImageJ? ''Tracing on Secondary Image'' is the answer to these questions: It allows you to feed SNT with pre-processed data on which the A*star search will operate. Here are two specific usages for this option:
*'''Frangi ''Vesselness'' filtering''' For certain datasets Frangi filtering ([https://link.springer.com/content/pdf/10.1007%252FBFb0056195.pdf Frangi et al. 1998]) is more effective than [[Tubeness]] at enhancing tube-like structures in the image. However, it is more computation intensive, and thus, less suitable to be adopted by the "compute-as-needed" approach used in Hessian-based analysis. Thus, one can import a pre-computed Frangi-filtered image using this option.
*'''Hessian-analysis at multiple scales''' Let's consider a structure formed simultaneously by very thick and very thin processes (e.g. axons and dendrites). To trace it one would need to adjust continuously the sigma parameter while tracing. Instead, to trace structures of variable diameters more effectively, one could load a copy of the current image as ''secondary image'', and assign different hessian parameters to both images.
Importantly, this option can be toggled at will, during tracing. Indeed, one can ping-pong between ''secondary image'' and main image simply, by pressing {{key|I}}, the shortcut for the ''Trace on Secondary '''I'''mage'' checkbox.
'''Secondary Image options''' can be specified in the ''gear'' drop-down menu, including commands for Loading/displaying the image file and the powerful ''Generate Secondary Filtered Image'' command:
[[Image:SNT-Tracing-On-Filtered-Image-Gear-Options.png|right|thumb|200px]]
[[Image:SNT-Generate-Filtered-Image-Prompt.png|right|thumb|200px]]
* '''Load Specified File''' Loads the filtered image specified in the ''File'' textbox.
* '''Generate Secondary Image''' Enables processing of the currently open image directly from SNT. Three routines are currently supported: ''Frangi'', ''Frangi (without Gaussian)'' and ''Tubeness''. Supports saving and display of the resulting image. To use the currently open image as the secondary image, choose ''None. Duplicate Primary Image''. Noteworthy: It is assumed that the current sigma value in the Auto-tracing widget reflects the size of structures to be filtered. If that is not the case, the sigma should be adjusted before running this command.
* '''Adjust Min-Max''' Sets the range of pixel intensities used by A* search.
* '''Show Cached image''' Displays the currently loaded filtered image in a separate window.
* '''Show Path in File Explorer''' Opens the directory containing the filtered image specified in the ''File'' textbox in the File Explorer GUI.
* '''Generate Filtered Image''' Enables processing of the currently open image directly from SNT. Three routines are currently supported: ''Frangi'', ''Frangi (without Gaussian)'' and ''Tubeness''. Supports saving and display of the resulting image. Noteworthy: It is assumed that the current sigma value in the Auto-tracing widget reflects the size of structures to be filtered. If that is not the case, the sigma should be adjusted before running this command.
* '''Show Cached image''' Displays the currently loaded filtered image in a separate window.
See the [[SNT:_Step-By-Step_Instructions#Generating_Filtered_Images|Generating Filtered Images]] walk-through for more details.
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